Frontiers in Probing Biomolecules

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Frontiers in Probing Biomolecules
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Objective

• To encourage chemist, physicist and basic
  science researcher involve in new technology
  development for bimolecular detection or address
  biologically important issues.

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What are the general problems that biochemists
are suffering?
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• Biomolecular recognition
• Protein activity analysis
• Fast kinetics
• Complexity of in vivo system
• Many others

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Suggested Major Subjects

• Chemical biology
• Ultra-fast kinetics
• New technology on bio-detection
• Bioconjugation and bioimaging

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Chemical Biology
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Adapted from Science 291, 23 Mar.2001
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Cell surface glyco-conjugates

• Cell-biomolecule interactions,
• The masking of receptors by cell-surface glycans,
  
• Markers in certain cancers,
• As ligands for proteins

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STn-antigen found in cancer cell
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Initial processing of the N-linked saccharide core
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.
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.
P. Sears and C.-H. Wong, Cell. Mol. Life Sci. 54
(1998) 223252
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Glycosphingolipid Storage Disorders

• The ability to manipulate glycoprotein and
  glycolipid biosynthetic pathways using specific
  glycosyltransferase and glycosidase inhibitor has
  enormous potential for drug development.

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human immunodeficiency virus (HIV)
Outer envelope a lipid bilayer with protruding
spikes (glycoprotein 120). Inside envelope
nucleocapsid Inside nucleocapsid viral genome
RNA, and reverse transcriptase.
http//www.boehringer-ingelheim.com/hiv/art/art_im
g.htm
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CD4 antigen on marcrophage and helper T cell
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The main components involved in viral
replication HIV genomic RNA, transfer RNA,
protease, integrase and reverse transcriptase.
Strategy to stop HIV replication !!!!!!
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How about SARS?
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Label-free biomolecule detection

• Reflectometric interference spectroscopy (RIFS)
• Surface Plasma resonance (SPR)
• Quartz crystal microbalance (QCM)
• Other new technology???

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SPR and its applications
Graph adapted from Biacore, Pharmacia Biotech
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• Left Protein DSD-PAGE analysis.
• Right Binding analysis of IgG-specifcVH
  single-domain protein to IgG by real-time surface
  plasmon resonance.

J. Mol. Biol. (1999) 290, 685-698
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Reflectometric interference spectroscopy (RIFS)
Reflectometric Interference Spectroscopy is based
on the Interference of light beams, which are
reflected at interfaces with different refractive
indices. A thin glass slide, typically coated
with an interference layer of 330nm SiO2, is
illuminated with white light. At each interface
the light beam is partly reflected. As the
reflected beams travel different optical paths, a
phase difference is introduced. Any change of
optical thickness (nd) will lead to changes in
the interference spectrum.
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http//barolo.ipc.uni-tuebingen.de/infomat/rifs/in
dex_en.html
Prof. Dr. G. Gauglitz, Institut für Physikalische
Chemie der Universität Tübingen
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Interactions of sense DNA with antisense
oligonucleotide
Anal. Chem.1999, 71,2850-2857
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Drug Screening and Development
Gene reconstruction of disease-related protein
Protein expression and purification
Immobilization of Protein
Natural product library
Peptide library
Chemical library
Identification of bound compounds
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Phage Display109-1010 clones containing of
human antibodies, which were inserted in g3p coat
protein of phage, were constructed.
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Ultra-fast Kinetics
Electron transfer, Protein dynamics, protein
refolding.
Best to include molecular simulation, theoretical
calculation
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Water Photolysis in Biology

• Photosystem II (PSII) is the heart of the
  photosynthetic process.
• Photosynthesis uses light energy to drive the
  oxidation of water at an oxygen evolving
  catalytic site within PSII.
• This multi-subunit complex is embedded in the
  thylakoid membranes of plants, algae and
  cyanobacteria.

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Protein structure

• 650 kDa dimeric multi-subunit complex
• The data strongly suggest that the OEC contains a
  cubane-like Mn3CaO4 cluster linked to a fourth Mn
  by a mono-m-oxo bridge.

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Protein structure of photosystem II from
cyanobacteria
James Barter et. al. (2004) Science, 303,1831.
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Oxygen-evolving center
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Light-induced electron transfer
Science 303, 19 Mar. 2004